The third eye - not so much the seat of the soul as a way to regulate circadian rhythms.

The "third eye"on a lizard - Wikipedia

The "third eye" was the seat of the soul, according to Rene Descartes, the French philosopher whose reductionist opinion of animals encouraged vivisection and other cruel animal experiments.
He couldn't have been more wrong. The third eye in reptiles is a functional adaptation which may allow them to "see" predators, like birds of prey, approaching from above. Its ability to function varies from species to species. In some it even has a lens and retina. In most reptiles the parietal eye doesn't have these but may be able "see" light and shade differences. There's a good description here.
The reptile parietal eye, connected to the pineal gland which is similar to the pineal gland deeper in the brain of mammals, responds to light and releases the hormone, melatonin, which regulates circadian rhythms like the sleep wake cycle. It influences the secretion of sex hormones too. And strangely it is the only bit of the middle brain that isn't paired. It's also got a good blood supply from a nearby artery.
In modern new age mysticism the third eye leads to  higher inner consciousness. With your third eye you see or experience stuff that ordinary non-enlightened humans cannot. Could your pet snake or lizard be on a higher plane that you are?

My Reptile Relationships survey is closing at the end of the month.